It would be cool to have the Master return as the leader of maybe even a group of timelords who managed to escape from the time lock. He may not even have been sent into the timelock - we never saw what exactly happened. He, possibly with some others, maybe got out just as the doorway closed. Though could either then go on the rampage for their own benefit, thinking themselves god-like, with the power to do what they want with the universe.
Or- maybe they aren't so bad and try to do some good in the universe, but the way they try to do that is by going to war with the Daleks, and/or the Rutans and/or Sontarans, which actually ends up causing some nasty side effects in the universe